Variant report

Variant	rs2885854
Chromosome Location	chr14:77782821-77782822
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr14:77782190-77782852	SK-N-SH	brain:	n/a	chr14:77782422-77782434 chr14:77782420-77782439
2	CTCF	chr14:77782131-77782889	SK-N-SH	brain:	n/a	chr14:77782429-77782437 chr14:77782417-77782438 chr14:77782423-77782439 chr14:77782424-77782437 chr14:77782422-77782440
3	CTCF	chr14:77782156-77782907	A549	lung:	n/a	chr14:77782429-77782437 chr14:77782417-77782438 chr14:77782423-77782439 chr14:77782424-77782437 chr14:77782422-77782440
4	CTCF	chr14:77782700-77782850	HCT-116	colon:	n/a	n/a
5	CTCF	chr14:77782740-77782890	GM12870	blood:	n/a	n/a
6	CTCF	chr14:77782740-77782890	HFF-Myc	foreskin:	n/a	n/a
7	CTCF	chr14:77782682-77782838	GM10266	blood:	n/a	n/a
8	CTCF	chr14:77782720-77782870	HPF	lung:	n/a	n/a
9	CTCF	chr14:77782720-77782870	BE2_C	brain:	n/a	n/a
10	SMC3	chr14:77782109-77782883	SK-N-SH	brain:	n/a	chr14:77782424-77782438

No.	Distal block	Cell Line	Cell type
1	chr14:77767017..77768635-chr14:77781868..77782985,9	MCF-7	breast:
2	chr14:77781065..77784774-chr14:77784883..77788972,8	K562	blood:
3	chr14:77782277..77784814-chr14:77790123..77792758,2	K562	blood:
4	chr14:77747430..77750741-chr14:77781891..77784413,3	MCF-7	breast:
5	chr14:77782500..77784938-chr14:77842054..77844042,2	MCF-7	breast:
6	chr14:77603673..77605750-chr14:77781536..77783991,2	MCF-7	breast:
7	chr14:77768914..77770037-chr14:77781888..77782887,4	MCF-7	breast:
8	chr14:77559718..77567556-chr14:77781210..77790475,16	MCF-7	breast:
9	chr14:77618596..77619216-chr14:77781871..77782869,3	MCF-7	breast:
10	chr14:77781658..77784050-chr14:77784883..77787153,4	K562	blood:
11	chr14:77766725..77768587-chr14:77781835..77783653,26	MCF-7	breast:

Variant related genes	Relation type
GSTZ1	TF binding region
POMT2	TF binding region
ENSG00000009830	Chromatin interaction
ENSG00000100580	Chromatin interaction
ENSG00000100577	Chromatin interaction
ENSG00000100583	Chromatin interaction
ENSG00000198894	Chromatin interaction
ENSG00000259164	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11624859	0.88[ASN][1000 genomes]
rs11626281	0.86[ASN][1000 genomes]
rs11627257	0.88[ASN][1000 genomes]
rs12431465	0.80[ASN][1000 genomes]
rs17105672	0.88[ASN][1000 genomes]
rs2042045	0.94[ASN][1000 genomes]
rs2111699	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2193594	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270421	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2363641	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2363642	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2363643	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759733	0.81[ASN][1000 genomes]
rs3815626	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147578	0.81[EUR][1000 genomes]
rs4147579	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4899650	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4903569	0.91[ASN][1000 genomes]
rs59630055	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61990299	0.88[ASN][1000 genomes]
rs6574367	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6574368	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67873774	0.88[ASN][1000 genomes]
rs7142812	0.94[ASN][1000 genomes]
rs7160188	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7160195	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975	0.89[EUR][1000 genomes]
rs8007615	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008449	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv902105	chr14:77764884-77801431	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv902106	chr14:77767978-77801431	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2885854	GSTZ1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77751400-77786200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr14:77770800-77785800	Weak transcription	K562	blood
3	chr14:77772600-77783800	Weak transcription	Dnd41	blood
4	chr14:77772600-77785800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:77772600-77786400	Weak transcription	Aorta	Aorta
6	chr14:77772800-77785800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr14:77773800-77786800	Weak transcription	Small Intestine	intestine
8	chr14:77774000-77783400	Weak transcription	Stomach Mucosa	stomach
9	chr14:77775800-77785600	Weak transcription	HUVEC	blood vessel
10	chr14:77775800-77786200	Weak transcription	Primary T cells from cord blood	blood
11	chr14:77776000-77783000	Weak transcription	Fetal Thymus	thymus
12	chr14:77776000-77786000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr14:77776000-77786400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:77776200-77786200	Weak transcription	Primary B cells from cord blood	blood
15	chr14:77776600-77785800	Weak transcription	Fetal Brain Male	brain
16	chr14:77777000-77784800	Weak transcription	Fetal Brain Female	brain
17	chr14:77777400-77785200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr14:77778000-77785800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr14:77778400-77784400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr14:77778800-77785800	Enhancers	Brain Cingulate Gyrus	brain
21	chr14:77779000-77783000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr14:77779000-77785800	Enhancers	Brain Anterior Caudate	brain
23	chr14:77779000-77786200	Enhancers	Fetal Intestine Large	intestine
24	chr14:77779200-77783000	Enhancers	Colon Smooth Muscle	Colon
25	chr14:77779200-77783200	Enhancers	Brain Substantia Nigra	brain
26	chr14:77779200-77784600	Enhancers	HepG2	liver
27	chr14:77779200-77785400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr14:77779200-77785800	Enhancers	Brain Angular Gyrus	brain
29	chr14:77779400-77783600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:77779400-77784200	Enhancers	Psoas Muscle	Psoas
31	chr14:77779400-77784600	Enhancers	Fetal Intestine Small	intestine
32	chr14:77779400-77785800	Enhancers	HMEC	breast
33	chr14:77779400-77786400	Enhancers	Fetal Muscle Leg	muscle
34	chr14:77779600-77785800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr14:77779800-77783400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr14:77780200-77783800	Enhancers	Adipose Nuclei	Adipose
37	chr14:77780400-77783600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:77780400-77784200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr14:77780800-77783600	Enhancers	Fetal Muscle Trunk	muscle
40	chr14:77781000-77783200	Weak transcription	NH-A	brain
41	chr14:77781200-77783200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr14:77781200-77785600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr14:77781200-77785800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr14:77781200-77786000	Weak transcription	Osteobl	bone
45	chr14:77781200-77786400	Weak transcription	Esophagus	oesophagus
46	chr14:77781400-77783200	Genic enhancers	Fetal Stomach	stomach
47	chr14:77781400-77783200	Weak transcription	HSMM	muscle
48	chr14:77781600-77783000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr14:77781600-77783000	Weak transcription	Left Ventricle	heart
50	chr14:77781600-77783200	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links